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(-) Description

Title :  CRYSTAL STRUCTURE OF THE EFFECTOR BINDING DOMAIN OF A BENM VARIANT (R156H,T157S)
 
Authors :  O. C. Ezezika, S. H. Craven, E. L. Neidle, C. Momany
Date :  09 Jun 06  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Lttr, Benm, Transcriptional Regulation, Catm, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. H. Craven, O. C. Ezezika, S. Haddad, R. A. Hall, C. Momany, E. L. Neidl
Inducer Responses Of Benm, A Lysr-Type Transcriptional Regulator From Acinetobacter Baylyi Adp1.
Mol. Microbiol. V. 72 881 2009
PubMed-ID: 19400783  |  Reference-DOI: 10.1111/J.1365-2958.2009.06686.X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HTH-TYPE TRANSCRIPTIONAL REGULATOR BENM
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: EFFECTOR BINDING DOMAIN
    Gene: BENM, BENR
    Mutation: YES
    Organism Scientific: ACINETOBACTER SP.
    Organism Taxid: 62977
    Strain: ADP1
    Synonym: BEN AND CAT OPERON TRANSCRIPTIONAL REGULATOR

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 12)

Asymmetric/Biological Unit (4, 12)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL
4SO45Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS B:148 , LYS B:155 , HIS B:156 , HOH B:594 , HOH B:660 , HOH B:717 , HOH B:722 , HOH B:789 , HOH B:852BINDING SITE FOR RESIDUE SO4 B 579
02AC2SOFTWARELYS A:90 , HIS A:116 , PRO A:117 , ASN A:118 , LEU A:119 , TYR A:281 , LYS B:129BINDING SITE FOR RESIDUE SO4 A 580
03AC3SOFTWAREVAL B:97 , GLY B:127 , THR B:128 , ARG B:146 , LEU B:147 , PRO B:196 , ASN B:202 , PHE B:203 , HOH B:603 , HOH B:664BINDING SITE FOR RESIDUE SO4 B 581
04AC4SOFTWAREHIS B:116 , PRO B:117 , ASN B:118 , LEU B:119BINDING SITE FOR RESIDUE SO4 B 582
05AC5SOFTWARELYS A:148 , ILE A:154 , LYS A:155 , HIS A:156 , HOH A:628BINDING SITE FOR RESIDUE SO4 A 583
06AC6SOFTWARELEU B:104 , ARG B:160 , ILE B:269 , TYR B:293 , HOH B:637 , HOH B:691BINDING SITE FOR RESIDUE ACT B 584
07AC7SOFTWARELEU A:104 , ARG A:160 , ILE A:269 , TYR A:293 , HOH A:629 , HOH A:639BINDING SITE FOR RESIDUE ACT A 585
08AC8SOFTWAREHIS B:206 , ASN B:209 , HOH B:678BINDING SITE FOR RESIDUE ACT B 586
09AC9SOFTWARESER A:157 , LEU A:159 , TYR A:286 , ARG A:290 , PRO A:301 , PRO A:302 , ASN A:303BINDING SITE FOR RESIDUE ACT A 587
10BC1SOFTWAREGLY A:127 , THR A:128 , ARG A:146 , ASN A:202 , PHE A:203 , HOH A:650 , HOH A:748BINDING SITE FOR RESIDUE ACT A 588
11BC2SOFTWARESER B:99 , ARG B:146 , VAL B:227BINDING SITE FOR RESIDUE CL B 589
12BC3SOFTWAREPHE B:102 , GLY B:103 , LEU B:104 , SER B:246 , SER B:249 , GLU B:296 , HOH B:765 , HOH B:781 , HOH B:872BINDING SITE FOR RESIDUE GOL B 590

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2H99)

(-) Cis Peptide Bonds  (9, 9)

Asymmetric/Biological Unit
No.Residues
1Tyr A:195 -Pro A:196
2Lys A:200 -Pro A:201
3Asn A:303 -Trp A:304
4Tyr B:195 -Pro B:196
5Lys B:200 -Pro B:201
6Glu B:300 -Pro B:301
7Pro B:301 -Pro B:302
8Pro B:302 -Asn B:303
9Asn B:303 -Trp B:304

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2H99)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2H99)

(-) Exons   (0, 0)

(no "Exon" information available for 2H99)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:215
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:215
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299     
           BENM_ACIAD    90 KTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW 304
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhh....eeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh...eeee.......hhhhhhhhhhhh......eeee..hhhhhhhhhhh....eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h99 A  90 KTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKHSLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW 304
                                    99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299     


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with BENM_ACIAD | O68014 from UniProtKB/Swiss-Prot  Length:304

    Alignment length:217
                                                                                                                                                                                                                                                 304 
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298     | 
           BENM_ACIAD    89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKRTLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNW-   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.hhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh....eeee........eeeeeeeeeeeeeeee..hhhhhhh....hhhhh...eeee.......hhhhhhhhhhhh......eeee..hhhhhhhhhhh....eeee.hhhhh....eeeee......eeeeeeeee....hhhhhhhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2h99 B  89 EKTIRIGFVGSLLFGLLPRIIHLYRQAHPNLRIELYEMGTKAQTEALKEGRIDAGFGRLKISDPAIKHSLLRNERLMVAVHASHPLNQMKDKGVHLNDLIDEKILLYPSSPKPNFSTHVMNIFSDHGLEPTKINEVREVQLALGLVAAGEGISLVPASTQSIQLFNLSYVPLLDPDAITPIYIAVRNMEESTYIYSLYETIRQIYAYEGFTEPPNWL 305
                                    98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 2H99)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2H99)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2H99)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (BENM_ACIAD | O68014)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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  2h99
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        BENM_ACIAD | O68014: 2f6g 2f6p 2f78 2f7a 2f8d 2f97 2h9b 3k1m 3k1n 3k1p 3m1e 4ihs 4iht

(-) Related Entries Specified in the PDB File

2f6p BENM-EBD SEMET
2f78 BENM-EBD + BENZOATE
2f7a BENM-EBD
2f7b CATM-EBD
2f8d BENM-EBD (HIGH PH)
2f97 BENM-EBD (HIGH PH)
2h98
2h9b
2h9q